[Debichem-devel] Looking for a mentor -- multiscale molecular modeling package MMB (and molmodel)

[Samuel Flores]

Hi Andreas and Andrius,

I guess we got stalled when the OpenMM guys declined to support debian
packages. At the time it was against my religion to fork supported
packages, but I have had a change of heart. I really only use the
neighborlisting function of OpenMM, and anyway I can always update the
local fork. So what I decided to do is just add the entire OpenMM
repository to the 3rdparty directory of my MMB git repo.  Also I put MMB on
the MIT license to comply with Debian's guidelines. Were these the main
stumbling blocks?

In the many months since we last spoke, I have also created a docker
container (samuelflores/mmb-ubuntu). I just set this  to compile MMB from
the 3rdparty directory -- a simple change which hopefully will build soon
on dockerhub. Assuming that goes well the Dockerfile should be a good model
for compiling with apt-get. There are a couple of people in Prague
contributing new code, and I have also taken on a couple of MS students so
there should be advances this summer on the code. So in short -- the
project has advanced substantially in the past few months and I think it is
in a good place for packaging.

I wonder if we can pick up the packaging project again?  Hopefully this
will go smoothly now that things have been worked on for a while.

With kind regards,

Sam

On Mon, Mar 4, 2019 at 1:59 PM Samuel Flores <samuelfloresc at gmail.com>
wrote:

> Hej Andreas,
>
> Sure, sounds great!  Thanks very much for offering to help. Sorry I have
> been so slow -- I have lots of administrative and pedagogical
> responsibility, and no students that might compile c++.
>
> I thought I saw OpenMM is already packaged. If not it should have an MIT
> license so might not even require permission from Simbios to package up.
> Molmodel is likewise also on MIT license, and I believe as maintainer I
> should have the authority to give permission to package that anyway. In any
> case Michael Sherman (former software architect at Simbios) or Joy Ku
> (current dissemination director) could clarify any permissions issue.
>
> With kind regards,
>
> Sam
>
> On 4 Mar 2019, at 13:15, Andreas Tille <tille at debian.org> wrote:
>
> Hi,
>
> On Wed, Feb 27, 2019 at 10:02:32AM +0200, Andrius Merkys wrote:
>
> Hi Samuel,
>
> On 2019-02-26 18:27, Samuel Flores wrote:
>
> I would like some help packaging MacroMoleculeBuilder (MMB) for
> distribution in Debian or Ubuntu. It is a mature piece of code, used to
> publish many scientific articles in structural bioinformatics and
> structural and molecular biology. It has been downloaded thousands of times.
>
>
> I would gladly help with the packaging of this modeling tool.
>
> I would be happy to change MMB's license to be compatible with this
> process.
>
>
> You are absolutely right to start with the license check. Debian accepts
> only those licenses that are compatible with Debian Free Software Guides
> [1]. You can find (incomplete) list of DFSG-compatible licenses here [2].
>
> [1] http://www.debian.org/social_contract#guidelines
> [2] https://wiki.debian.org/DFSGLicenses
>
> MMB requires OpenMM, simbody, and SeqAn, I believe all of these are
> already packaged. It also requires SimTK molmodel which is not packaged --
> I am the maintainer of molmodel and would like to package this as well.
> Molmodel is not hard to compile, but it does use cmake.
>
>
> OpenMM and molmodel are not yet in Debian, AFAIK. Thus they have to be
> packaged before the MMB. To start with, I would suggest reading the
> introduction to packaging [3], as Andrey has advised.
>
>
> I'd recommend to discuss this with DebiChem team (list in CC)
>
> Andrius Merkys
> Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
> LT-10257 Vilnius, Lithuania
>
>
> See you soon at Debian Med sprint
>
>      Andreas.
>
> --
> http://fam-tille.de
>
>
>
>
>
> *Samuel Coulbourn Flores, Docent*Dean of the Swedish National Graduate
> School in Medical Bioinformatics
> *Studierektor för den nationella forskarskolan inom
> medicinsk bioinformatik*
>
> Department of Biochemistry and Biophysics
> Stockholm University
>
> Visiting:
> SciLifeLab A6220 (Alpha Tr. 6)
>
> Deliveries:
> Samuel Flores
> Stockholms Universitet, Org # 202100-3062
> Tomtebodavägen 23a
> 171 65 Solna
> SWEDEN
>
> Mobil: +46.706000464
> Mexank: 0816-3949
> skype: samuelfloresc
> QQ: 3236579471
>
>
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